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  2. Implementation of molecular breeding in rye (Secale cereale L.) improvement programs depends on the availability of high-density molecular linkage maps. However, the number of sequence-specific PCR-based markers ...

    Authors: Hanna Bolibok-Brągoszewska, Katarzyna Heller-Uszyńska, Peter Wenzl, Grzegorz Uszyński, Andrzej Kilian and Monika Rakoczy-Trojanowska
    Citation: BMC Genomics 2009 10:578
    Content type: Research article Published on:

  3. Alternative splicing (AS) is a primary mechanism of functional regulation in the human genome, with 60% to 80% of human genes being alternatively spliced. As part of the bovine genome annotation team, we have ...

    Authors: Elsa Chacko and Shoba Ranganathan
    Citation: BMC Genomics 2009 10(Suppl 3):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  4. DNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and mi...

    Authors: Piroon Jenjaroenpun and Vladimir A Kuznetsov
    Citation: BMC Genomics 2009 10(Suppl 3):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  5. Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test t...

    Authors: Guillaume Le Mignon, Colette Désert, Frédérique Pitel, Sophie Leroux, Olivier Demeure, Gregory Guernec, Behnam Abasht, Madeleine Douaire, Pascale Le Roy and Sandrine Lagarrigue
    Citation: BMC Genomics 2009 10:575
    Content type: Research article Published on:

  6. An essential driving component in the co-evolution of plants and insects is the ability to produce and handle bioactive compounds. Plants produce bioactive natural products for defense, but some insects detoxi...

    Authors: Mika Zagrobelny, Karsten Scheibye-Alsing, Niels Bjerg Jensen, Birger Lindberg Møller, Jan Gorodkin and Søren Bak
    Citation: BMC Genomics 2009 10:574
    Content type: Research article Published on:

  9. Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the mo...

    Authors: George E Liu, Mario Ventura, Angelo Cellamare, Lin Chen, Ze Cheng, Bin Zhu, Congjun Li, Jiuzhou Song and Evan E Eichler
    Citation: BMC Genomics 2009 10:571
    Content type: Research article Published on:

  10. Saturated brines are extreme environments of low diversity. Salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in...

    Authors: Lejla Pašić, Beltran Rodriguez-Mueller, Ana-Belen Martin-Cuadrado, Alex Mira, Forest Rohwer and Francisco Rodriguez-Valera
    Citation: BMC Genomics 2009 10:570
    Content type: Research article Published on:

  12. It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/o...

    Authors: Keiichi Mochida, Taku Furuta, Kaworu Ebana, Kazuo Shinozaki and Jun Kikuchi
    Citation: BMC Genomics 2009 10:568
    Content type: Research article Published on:

  13. Combating the action of plant pathogenic microorganisms by mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since two decades. The fungal genus Tric...

    Authors: Verena Seidl, Lifu Song, Erika Lindquist, Sabine Gruber, Alexeji Koptchinskiy, Susanne Zeilinger, Monika Schmoll, Pedro Martínez, Jibin Sun, Igor Grigoriev, Alfredo Herrera-Estrella, Scott E Baker and Christian P Kubicek
    Citation: BMC Genomics 2009 10:567
    Content type: Research article Published on:

  14. While attempting to reanalyze published data from Agilent 4 × 44 human expression chips, we found that some of the 60-mer olignucleotide features could not be interpreted as representing single human genes. Fo...

    Authors: E Michael Gertz, Kundan Sengupta, Michael J Difilippantonio, Thomas Ried and Alejandro A Schäffer
    Citation: BMC Genomics 2009 10:566
    Content type: Research article Published on:

  15. Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expressio...

    Authors: Kai N Stölting, Gerrit Gort, Christian Wüst and Anthony B Wilson
    Citation: BMC Genomics 2009 10:565
    Content type: Research article Published on:

  16. Venom variation occurs at all taxonomical levels and can impact significantly upon the clinical manifestations and efficacy of antivenom therapy following snakebite. Variation in snake venom composition is tho...

    Authors: Nicholas R Casewell, Robert A Harrison, Wolfgang Wüster and Simon C Wagstaff
    Citation: BMC Genomics 2009 10:564
    Content type: Research article Published on:

  17. Despite many studies on the biogenesis, molecular structure and biological functions of microRNAs, little is known about the transcriptional regulatory mechanisms controlling the spatiotemporal expression patt...

    Authors: Tong J Gu, Xiang Yi, Xi W Zhao, Yi Zhao and James Q Yin
    Citation: BMC Genomics 2009 10:563
    Content type: Research article Published on:

  18. Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable a...

    Authors: Antonio Cabrera, Alex Kozik, Werner Howad, Pere Arus, Amy F Iezzoni and Esther van der Knaap
    Citation: BMC Genomics 2009 10:562
    Content type: Research article Published on:

  19. Single nucleotide polymorphisms (SNPs) have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution ...

    Authors: Jun Wang, Min Lin, Andrew Crenshaw, Amy Hutchinson, Belynda Hicks, Meredith Yeager, Sonja Berndt, Wen-Yi Huang, Richard B Hayes, Stephen J Chanock, Robert C Jones and Ramesh Ramakrishnan
    Citation: BMC Genomics 2009 10:561
    Content type: Methodology article Published on:

  20. Sequence identification of ESTs from non-model species offers distinct challenges particularly when these species have duplicated genomes and when they are phylogenetically distant from sequenced model organis...

    Authors: Weizhong Li, Andrew Y Gracey, Luciane Vieira Mello, Andrew Brass and Andrew R Cossins
    Citation: BMC Genomics 2009 10:560
    Content type: Research article Published on:

  21. To enhance capabilities for genomic analyses in rainbow trout, such as genomic selection, a large suite of polymorphic markers that are amenable to high-throughput genotyping protocols must be identified. Expr...

    Authors: Cecilia Castaño Sánchez, Timothy PL Smith, Ralph T Wiedmann, Roger L Vallejo, Mohamed Salem, Jianbo Yao and Caird E Rexroad III
    Citation: BMC Genomics 2009 10:559
    Content type: Research article Published on:

  22. MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multipl...

    Authors: Erica Mica, Viviana Piccolo, Massimo Delledonne, Alberto Ferrarini, Mario Pezzotti, Cesare Casati, Cristian Del Fabbro, Giorgio Valle, Alberto Policriti, Michele Morgante, Graziano Pesole, M Enrico Pè and David S Horner
    Citation: BMC Genomics 2009 10:558
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Genomics 2010 11:109

  23. Human adenoviruses (HAdV) are causing a broad spectrum of diseases. One of the most severe forms of adenovirus infection is a disseminated disease resulting in significant morbidity and mortality. Several repo...

    Authors: Soeren Hofmayer, Ijad Madisch, Sebastian Darr, Fabienne Rehren and Albert Heim
    Citation: BMC Genomics 2009 10:557
    Content type: Research article Published on:

  24. Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation. These microvesicles can mediate communication between cel...

    Authors: Bok Sil Hong, Ji-Hoon Cho, Hyunjung Kim, Eun-Jeong Choi, Sangchul Rho, Jongmin Kim, Ji Hyun Kim, Dong-Sic Choi, Yoon-Keun Kim, Daehee Hwang and Yong Song Gho
    Citation: BMC Genomics 2009 10:556
    Content type: Research article Published on:

  25. The next generation sequencing technologies provide new options to characterize the transcriptome and to develop affordable tools for functional genomics. We describe here an innovative approach for this purpo...

    Authors: Diana Bellin, Alberto Ferrarini, Antonio Chimento, Olaf Kaiser, Natasha Levenkova, Pascal Bouffard and Massimo Delledonne
    Citation: BMC Genomics 2009 10:555
    Content type: Methodology article Published on:

  26. Post-translational histone modifications (PTMs) and their specific distribution on genes play a crucial role in the control of gene expression, but the regulation of their dynamics upon gene activation and dif...

    Authors: Katharina Sarah Heyse, Susanne Erika Weber and Hans-Joachim Lipps
    Citation: BMC Genomics 2009 10:554
    Content type: Research article Published on:

  29. Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s) or mutation(s) ...

    Authors: Aurélie Bonin, Margot Paris, Guillaume Tetreau, Jean-Philippe David and Laurence Després
    Citation: BMC Genomics 2009 10:551
    Content type: Research article Published on:

  30. The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposu...

    Authors: Mathieu Gautier, Laurence Flori, Andrea Riebler, Florence Jaffrézic, Denis Laloé, Ivo Gut, Katayoun Moazami-Goudarzi and Jean-Louis Foulley
    Citation: BMC Genomics 2009 10:550
    Content type: Research article Published on:

  31. Polycomb group (PcG) proteins maintain expression pattern of genes set early during development. Although originally isolated as regulators of homeotic genes, PcG members play a key role in epigenetic mechanism t...

    Authors: Ramamoorthy Senthilkumar and Rakesh K Mishra
    Citation: BMC Genomics 2009 10:549
    Content type: Research article Published on:

  32. The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the mammary epithelium. Our aim was to analyse...

    Authors: Stefanie Avril-Sassen, Leonard D Goldstein, John Stingl, Cherie Blenkiron, John Le Quesne, Inmaculada Spiteri, Konstantina Karagavriilidou, Christine J Watson, Simon Tavaré, Eric A Miska and Carlos Caldas
    Citation: BMC Genomics 2009 10:548
    Content type: Research article Published on:

  33. De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L.) is a major challenge both in terms of experimental feasibility and costs. The emergence and breatht...

    Authors: Burkhard Steuernagel, Stefan Taudien, Heidrun Gundlach, Michael Seidel, Ruvini Ariyadasa, Daniela Schulte, Andreas Petzold, Marius Felder, Andreas Graner, Uwe Scholz, Klaus FX Mayer, Matthias Platzer and Nils Stein
    Citation: BMC Genomics 2009 10:547
    Content type: Methodology article Published on:

  34. Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowle...

    Authors: Antoine D Rolland, Jean-Jacques Lareyre, Anne-Sophie Goupil, Jérôme Montfort, Marie-Jo Ricordel, Diane Esquerré, Karine Hugot, Rémi Houlgatte, Fréderic Chalmel and Florence Le Gac
    Citation: BMC Genomics 2009 10:546
    Content type: Research article Published on:

  35. Sharing a common ErbB/HER receptor signaling pathway, heregulin (HRG) induces differentiation of MCF-7 human breast cancer cells while epidermal growth factor (EGF) elicits proliferation. Although cell fates r...

    Authors: Yuko Saeki, Takaho Endo, Kaori Ide, Takeshi Nagashima, Noriko Yumoto, Tetsuro Toyoda, Harukazu Suzuki, Yoshihide Hayashizaki, Yoshiyuki Sakaki and Mariko Okada-Hatakeyama
    Citation: BMC Genomics 2009 10:545
    Content type: Research article Published on:

  37. The deposition of unconjugated bilirubin (UCB) in selected regions of the brain results in irreversible neuronal damage, or Bilirubin Encephalopathy (BE). Although UCB impairs a large number of cellular functi...

    Authors: Raffaella Calligaris, Cristina Bellarosa, Rossana Foti, Paola Roncaglia, Pablo Giraudi, Helena Krmac, Claudio Tiribelli and Stefano Gustincich
    Citation: BMC Genomics 2009 10:543
    Content type: Research article Published on:

  38. Information generated via microarrays might uncover interactions between the mammary gland and Streptococcus uberis (S. uberis) that could help identify control measures for the prevention and spread of S. uberis

    Authors: Kasey M Moyes, James K Drackley, Dawn E Morin, Massimo Bionaz, Sandra L Rodriguez-Zas, Robin E Everts, Harris A Lewin and Juan J Loor
    Citation: BMC Genomics 2009 10:542
    Content type: Research article Published on:

  40. Interest in lycopene metabolism and regulation is growing rapidly because accumulative studies have suggested an important role for lycopene in human health promotion. However, little is known about the molecu...

    Authors: Qiang Xu, Keqin Yu, Andan Zhu, Junli Ye, Qing Liu, Jianchen Zhang and Xiuxin Deng
    Citation: BMC Genomics 2009 10:540
    Content type: Research article Published on:

  41. The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to ...

    Authors: Martin Trick, Soo-Jin Kwon, Su Ryun Choi, Fiona Fraser, Eleni Soumpourou, Nizar Drou, Zhi Wang, Seo Yeon Lee, Tae-Jin Yang, Jeong-Hwan Mun, Andrew H Paterson, Christopher D Town, J Chris Pires, Yong Pyo Lim, Beom-Seok Park and Ian Bancroft
    Citation: BMC Genomics 2009 10:539
    Content type: Research article Published on:

  42. Previous investigations from our laboratory were largely focused on the genome organization of vertebrates. We showed that these genomes are mosaics of isochores, megabase-size DNA sequences that are fairly ho...

    Authors: Rosalia Cammarano, Maria Costantini and Giorgio Bernardi
    Citation: BMC Genomics 2009 10:538
    Content type: Research article Published on:

  43. In prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-direct...

    Authors: Albert Pallejà, Santiago García-Vallvé and Antoni Romeu
    Citation: BMC Genomics 2009 10:537
    Content type: Research article Published on:

  44. The repABC plasmid family, which is extensively present within Alphaproteobacteria, and some secondary chromosomes of the Rhizobiales have the particular feature that all the elements involved in replication and ...

    Authors: Santiago Castillo-Ramírez, Jorge F Vázquez-Castellanos, Víctor González and Miguel A Cevallos
    Citation: BMC Genomics 2009 10:536
    Content type: Research article Published on:

  46. Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive...

    Authors: Tiratha Raj Singh, Georgia Tsagkogeorga, Frédéric Delsuc, Samuel Blanquart, Noa Shenkar, Yossi Loya, Emmanuel JP Douzery and Dorothée Huchon
    Citation: BMC Genomics 2009 10:534
    Content type: Research article Published on:

  47. The Syndermata (Rotifera+Acanthocephala) is one of the best model systems for studying the evolutionary origins and persistence of different life styles because it contains a series of lineage-specific life hi...

    Authors: Gi-Sik Min and Joong-Ki Park
    Citation: BMC Genomics 2009 10:533
    Content type: Research article Published on:

  48. Human endogenous retroviruses (HERV) constitute approximately 8% of the human genome and have long been considered "junk". The sheer number and repetitive nature of these elements make studies of their express...

    Authors: Christoffer Nellåker, Fang Li, Fredrik Uhrzander, Joanna Tyrcha and Håkan Karlsson
    Citation: BMC Genomics 2009 10:532
    Content type: Research article Published on:

  50. Array genomic hybridization is being used clinically to detect pathogenic copy number variants in children with intellectual disability and other birth defects. However, there is no agreement regarding the kin...

    Authors: JM Friedman, Shelin Adam, Laura Arbour, Linlea Armstrong, Agnes Baross, Patricia Birch, Cornelius Boerkoel, Susanna Chan, David Chai, Allen D Delaney, Stephane Flibotte, William T Gibson, Sylvie Langlois, Emmanuelle Lemyre, H Irene Li, Patrick MacLeod…
    Citation: BMC Genomics 2009 10:526
    Content type: Research article Published on:

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